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Bond-Graph Modelling and Causal Analysis of Biomolecular Systems

  • Peter J. Gawthrop
Chapter

Abstract

Bond graph modelling of the biomolecular systems of living organisms is introduced. Molecular species are represented by non-linear C components and reactions by non-linear two-port R components. As living systems are neither at thermodynamic equilibrium nor closed, open and non-equilibrium systems are considered and illustrated using examples of biomolecular systems. Open systems are modelled using chemostats: chemical species with fixed concentration. In addition to their role in ensuring that models are energetically correct, bond graphs provide a powerful and natural way of representing and analysing causality. Causality is used in this chapter to examine the properties of the junction structures of biomolecular systems and how they relate to biomolecular concepts.

Keywords

Bond Graph Junction Structure Stoichiometric Matrix Kernel Matrice Biomolecular System 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

Peter Gawthrop would like to thank the Melbourne School of Engineering for its support via a Professorial Fellowship. He would also like to thank Michael Pan and Joe Cursons for their close reading of the draft chapter.

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Copyright information

© Springer International Publishing Switzerland 2017

Authors and Affiliations

  1. 1.Systems Biology LaboratoryMelbourne School of Engineering, University of MelbourneMelbourneAustralia

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